Fix failing specs that break in PathUtil.relative_path

@bbatsov @yujinakayama I found the problem with the specs.

When `Include` and `Exclude` configuration parameters were added in `default.yml`, some specs could no longer run with the default buffer name `"(string)"` or `"example.rb"`. They need an absolute path.

Fixing this revealed some other problems; that `app/models` must be changed to `app/models/*.rb` for example. Also, the paths given in `Include` are not interpreted as relative to the configuration file. They should be.

This PR should make all the specs pass again, but some work on the handling of paths from configuration is still needed.